Hi Mark,
I'm sorry, I assume you'll understand that I've carried out all the steps
before an EM run.
David said is because the coordinates are on top of each other, I'll
appreciate any more specific advice on how to fix this.
Meanwhile, I'll try Martin's advice on making the water flexible.
Rgds
John
From: Mark Abraham <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Subject: Re: [gmx-users] potential energy =nan
Date: Wed, 20 Jun 2007 23:09:03 +1000
Sheyore Omovie wrote:
I am doing an Energy Minimisation run for two polypeptides in a box. I get
the range checking error, variable ci= .... and the simulation crashes.
After changing ns_type to simple, the simulation is running, but very
slowly and the first few steps return Epot=nan.
What could I have done wrong?
It's hard to tell from your description, since an energy minimization is
not a simulation... but please try following this general scheme
http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation
Mark
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface
or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_________________________________________________________________
Picture this share your photos and you could win big!
http://www.GETREALPhotoContest.com?ocid=TXT_TAGHM&loc=us
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
